He still thinks they should all be imprisoned. All of them including Bethany. Who has shown herself nothing like his Magisters.
At first, yeah. But then you get:
Anders: You must know that the Templars are wrong.
Fenris: Must I? I see Templars trying to control what they have good reason to fear.
Anders: But they go too far.
Fenris: Talk to Hawke about her mother. Ask her who went "too far".
Anders: You can't hold all mages responsible for that!
Fenris: It doesn't take all mages to cause this. Only the weak ones.
Anders: Not all mages are weak.
Fenris: True. Bethany, for one, is not weak / Hawke, for one, is not weak. (If Hawke is a mage)
Anders: I notice you didn't mention me.
Fenris: No.
Anders: I'll prove to you that I'm not weak
Fenris: Prove it to yourself. You aren't fooling anyone else.
It seems like he trusts Bethany (or Hawke) to not use blood magic or become abominations but others haven't proven themselves to him so he thinks they need to be kept contained.
I don't think he's unaware I think he's just respecting who Hawke is.
I disagree. No one in your party gains or loses approval when they are not physically present. Let's take Anders as an example. Do you think he would just 'respect who Hawke is' and be grateful that he's not present while Hawke goes around acting like a templar and killing/recapturing all apostates she encounters? I think Anders would hate what's happening regardless and yet watch the fact he doesn't react to it in the slightest and you can still be his best friend if you leave him at home on these missions. It's not being pleased not to be involved and respecting Hawke's decisions. It's the fact that no companion at all has their friendship meter affected by what happens when they are not standing there.
And actually, Fenris will stand by you if you have maxed out his rivalry meter...which you can do by 'rubbing in his face all the time' that you are 100% pro-mage.